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P4Projects in ABI
Page P4Projects Material Please download the template cmake project and use it for four project. In the Readme file you should find all the information you need …
09 Aug 2023 - 17:03, UnknownUser
PMSB_OpenMS_2011 in ABI
Projektmanagement im Softwarebereich OpenMS 2011 Wiki Seite zum Praktikum Projektmanagement im Softwarebereich http://www.openms.de/ OpenMS 2011. Zeitplan…
09 Aug 2023 - 17:03, UnknownUser
PMSB_OpenMS_2012 in ABI
Projektmanagement im Softwarebereich OpenMS 2012 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich OpenMS. Projektgruppen …
09 Aug 2023 - 17:03, UnknownUser
PMSB_Seqan_2010 in ABI
Projektmanagement im Softwarebereich Seqan 2010 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich Seqan. Aufteilung auf di…
09 Aug 2023 - 17:03, UnknownUser
PMSB_Seqan_2011 in ABI
Projektmanagement im Softwarebereich Seqan 2011 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich Seqan. Aufteilung auf di…
09 Aug 2023 - 17:03, UnknownUser
PMSB_Seqan_2012 in ABI
Projektmanagement im Softwarebereich SeqAn 2012 Das ist die vorläufige Wiki Seite zum Praktikum Projektmanagement im Softwarebereich SeqAn. Teilnehmer Name…
09 Aug 2023 - 17:03, UnknownUser
PMSB_Seqan_2013 in ABI
Projektmanagement im Softwarebereich SeqAn 2013 Dies ist die Wiki Seite zum Praktikum Projektmanagement im Softwarebereich SeqAn. Alle Zeiten sind s.t. also w…
09 Aug 2023 - 17:03, UnknownUser
PMSB_Seqan_2014 in ABI
Projektmanagement im Softwarebereich, SoSe 2014 (19588a und 19588b) * Einführung in Software Engineering am Freitag entfällt leider! Dies ist die Wiki Seite z…
09 Aug 2023 - 17:03, UnknownUser
PMSB_Seqan_2015 in ABI
Projektmanagement im Softwarebereich, SoSe 2015 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum
09 Aug 2023 - 17:03, UnknownUser
PMSB_Seqan_2016 in ABI
Projektmanagement im Softwarebereich, SoSe 2016 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum
09 Aug 2023 - 17:03, UnknownUser
PMSB_Seqan_2017 in ABI
Projektmanagement im Softwarebereich, SoSe 2017 (19401511 (S) und 19401513 (P)) Dies ist die Wiki Seite zum Praktikum
09 Aug 2023 - 17:03, UnknownUser
PMSB_Seqan_2018 in ABI
Projektmanagement im Softwarebereich, SoSe 2018 Dies ist die Wiki Seite zum Praktikum
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2013_BlastX in ABI
Page PSMB_Seqan_2013_BlastX Hintergrund: NGS Daten in Proteindatenbanken Next Generation Sequencing (NGS) Daten werden heute für unterschiedlichste Aufgaben verw…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2013_Lagan in ABI
Page PSMB_Seqan_2013_Lagan Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntniss…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2013_NGS_Data_Cleansing in ABI
NGS Data Postprocessing Hintergrund Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichnet man Sequenzierverfahren, die in ver…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2013_NGS_Data_Cleansing_New in ABI
NGS Data Postprocessing Hintergrund Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichnet man Sequenzierverfahren, die in ver…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2013_NGS_Data_Cleansing_Progress in ABI
Progress
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2013_NGS_Quality_Control in ABI
Page PSMB_Seqan_2013_NGS_Quality_Control Hintegrund: NGS Quality Control Als Next Generation Sequencing (NGS) oder auch High Througput Sequencing (HTS) bezeichne…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2013_NGS_Quality_Control_Details_Features in ABI
PSMB_Seqan_2013_NGS_Quality_Control_Details_Features Our application will read fastq files and collect statistical data about its content. The input itself will n…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2013_PEMer in ABI
Page PSMB_Seqan_2013_PEMer PEMer overview, Figure 1 from (Korbel et al., 2009). Hintergrund: Paired End Signaturen und Strukturvarianten Als Strukturvarianten be…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2013_Suboptimal_Alignments in ABI
Page PSMB_Seqan_2013_Suboptimal_Alignments Hintergrund: Suboptimale Alignments Lokale Alignments sind eine mächtige Methode um Sequenzhomologien zwischen zwei Se…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2013_UBlast in ABI
Schnelle Blastsuche durch Datenbank Clustering Hintergrund: Der Vergleich von Next Generation Sequencing (NGS) Daten gegen DNA oder Proteindatenbanken gehoert …
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2013_UBlast_Progress in ABI
Progress
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2014_SNP_caller in ABI
PSMB_Seqan_2014_SNP_caller Hintergrund Die häufigste und kleinste mögliche genomische Variation ist der Single Nucleotide Polymorphism. Nach dem Mapping von Read…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2014_large_insertd in ABI
PSMB_Seqan_2014_large_insertd Hintergrund Lange Sequenzstücke, die im Donor aber nicht in der Referenz enthalten sind, lassen sich nur schwer mit einzelnen Reads…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2014_mapper in ABI
PSMB_Seqan_2014_mapper Hintergrund Der erste Schritt ein einer Pipeline zur Analyse von Genomvarianten ist das Read Mapping. Dabei soll für jeden NGS Read eigent…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2014_overview in ABI
PSMB_Seqan_2014_overview Im PSMB SeqAn 2014 geht es darum, eine einfach Pipeline zur Variantenanalyse aufzubauen. Hintergrund Insbesondere für das menschliche Ge…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2014_small_indels in ABI
PSMB_Seqan_2014_small_indels Hintergrund Neben SNPs sind kleine Insertionen und Deletionen (indels) eine Klasse wichtiger genomischer Varianten. Für die Suche so…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2015_p2 in ABI
Page PSMB_Seqan_2015_p2 Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntnisse b…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2015_p3 in ABI
PSMB_Seqan_2015_p3 Einleitung Eines der bekanntesten und meist genutzten Programme im Kontext der Bioinformatik ist NCBI Blast. Blast ist ein heuristisches Tool …
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2015_p4 in ABI
PSMB_Seqan_2015_p4 Introduction Trypsin is a serine protease found in the digestive system of many vertebrates, where it hydrolyses proteins. It cleaves peptide …
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2015_p5 in ABI
PSMB_Seqan_2015_p5 Introduction The q gram(k mer) Index in seqan allows looking up k mers over the index in constant time. However it has two limitations. The fi…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2015_palign in ABI
PSMB_Seqan_2015_palign Einleitung Paarweise Sequenzalignments liefern wertvolle biologische Informationen über die Identität zweier Sequenzen. Entsprechend w…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2016_p1 in ABI
PSMB_Seqan_2016_p1 PMSB Project with possible Bachelor Project. Some experience with Javascript is required, some experience with C or C is recommended. Introdu…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2016_p2 in ABI
Assessment of off target effects of non coding RNAs Bioinformatics or computational biology is one of the fast growing and most exciting fields in science. Throug…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2016_p3 in ABI
PSMB_Seqan_2016_p3 Hintergrund Der erste Schritt ein einer Pipeline zur Analyse von Genomvarianten ist das Read Mapping. Dabei soll für jeden NGS Read eigentlich…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2016_p4 in ABI
PSMB_Seqan_2016_p4 In this project you will implement the typical Needleman Wunsch Algorithm, but with a few twists that will hopefully allow
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2016_p5 in ABI
Add BAM support to SeqAn SequenceFile In this project you will be asked to write an interface that will help the Sequence IO of SeqAn to seamlessly read SAM/BAM f…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2016_p6 in ABI
LArge Genome AligNer (LAGAN) Hintergrund: Alignieren Genomischer Sequenzen Durch das vergleichen zweier Genome unterschiedlicher Organismen können neue Erkenntni…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2017_p1 in ABI
Assessment of off target effects of non coding RNAs Bioinformatics or computational biology is one of the fast growing and most exciting fields in science. Throug…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_2017_webassembly in ABI
PSMB_Seqan_2017_webassembly PMSB Project at the intersection of C , High performance computing and modern web technologies. Has the possibility to be continued as…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_IBF in ABI
Auswertugn von Binning directories mit Hilfe von Interleaved Bloom filters Hintergrund: Filtern von NGS reads in bins In dem projekt soll (zufällig generierte) …
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_MF in ABI
In this project a simple motif discovery algorithm should be implemented in SeqAn. Background The goal of motif "finding is the detection of novel, unknown sign…
09 Aug 2023 - 17:03, UnknownUser
PSMB_Seqan_fft in ABI
Detection of homologous regions with FFT Given a set of sequences your task is to compute homologous segments for all pairs of the input set. The detection of hom…
09 Aug 2023 - 17:03, UnknownUser
ParallelSuffixArray in ABI
Parallel Suffix Array Construction Area Substring Indices Topic Das Suffix Array speichert die Anfänge aller Suffixe eines (oder mehrerer) Texte in lexikographi…
09 Aug 2023 - 17:03, UnknownUser
PhylogeneticAnalsysis in ABI
Phylogenie News Skript wird nach der Vorlesung aktualisiert. Abweichungen zwischen Material der Vorlesung und aktuellem Skript halten sich in Grenzen. Vorlesung…
09 Aug 2023 - 17:03, UnknownUser
Phylogeny in ABI
Vorlesungen Phylogenetische Analyse Date Lecture* *Materials 16.12.2010 Branch and Cut Intro b and c.pdf, Webpage http://www2.iwr.uni heidelberg.de…
09 Aug 2023 - 17:03, UnknownUser
PiSWS10 in ABI
Projektmanagement im Softwarebereich (WS 10/11) An fünf Terminen im Wintersemester finden jeweils 14 Uhr Veranstaltungen als Vorbereitung auf das eigentliche Soft…
09 Aug 2023 - 17:03, UnknownUser
Praktikum in ABI
Praktikum Das Blockpraktikum findet vom 5.12. bis 16.12.2011 statt. Der Bericht ist bis zum 23.12.2011 per Mail an rokrause #64;fu berlin.de einzureichen Zuteil…
09 Aug 2023 - 17:03, UnknownUser
ProgrammingExerciseOptiWS12 in ABI
General information for programming exercises * We will continue working in the repository from the Algorithms lecture. To discriminate the exercise files we a…
09 Aug 2023 - 17:03, UnknownUser
ProgrammingExerciseOptiWS13 in ABI
Short Overview The practical exercises for the lecture Optimization won't be programming exercises. Mostly you have to get familiar with an LP Solver, try to solv…
09 Aug 2023 - 17:03, UnknownUser
ProgrammingExercises in ABI
General information for programming exercises * Each group gets access to a svn directory at https://svn.imp.fu berlin.de/agbio/AlgorithmsWS12/GroupX (Enter yo…
09 Aug 2023 - 17:03, UnknownUser
ProgrammingExercisesWS13 in ABI
General information for programming exercises * Each group gets access to a svn directory at https://svn.imp.fu berlin.de/agbio/AlgorithmsWS13/GroupX * The…
09 Aug 2023 - 17:03, UnknownUser
ProgrammingExercisesWS14 in ABI
General information for programming exercises * Please note, that there will be an optional C crash course on Friday during the exercises. * Please, fill…
09 Aug 2023 - 17:03, UnknownUser
ProgrammingGroupList in ABI
Page ProgrammingGroupList Enter the account names and your group id into one of the two tables for the practical exercises in the second programming exercise week…
09 Aug 2023 - 17:03, UnknownUser
ProgressAicheFall2010 in ABI
Progress report Stephan Aiche fall 2010 OpenMS * generic labeling framework for MSSimulator is finished * OpenMS 1.7 released * parallel implementation …
09 Aug 2023 - 17:03, UnknownUser
ProgressAicheSpring2010 in ABI
Progress report Stephan Aiche fall 2010 OpenMS * new Model for Elution profiles in MSSimulator * started implementation of generic labeling framework (loca…
09 Aug 2023 - 17:03, UnknownUser
ProgressAicheSpring2011 in ABI
Progress report Stephan Aiche sprint 2011 Protease Kinetics * MSSimulator Paper published in JPR * prepared thesis outline AicheOutlineDraft * implement…
09 Aug 2023 - 17:03, UnknownUser
ProgressAndreotti2010 in ABI
Progress report Sandro Andreotti fall 2010 Work performed last 6 months * Several programming tasks were performed for the major revision of the ANTILOPE …
09 Aug 2023 - 17:03, UnknownUser
ProgressReportEmde-04-2010 in ABI
Page ProgressReportEmde 04 2010 Progress report Accomplishments in the last six months: General: * Read many papers on variant detection, notes taken here. …
09 Aug 2023 - 17:03, UnknownUser
ProgressReportEmde-05-2011 in ABI
Page ProgressReportEmde 05 2011 Progress Report (under construction) Accomplishments in the last six months: SplazerS: * redid single end read simulation (co…
09 Aug 2023 - 17:03, UnknownUser
ProgressReportEmde-10-2010 in ABI
Page ProgressReportEmde 10 2010 Progress Report Accomplishments in the last six months: Split read mapping: * Finished implementation of splitRazers, poster…
09 Aug 2023 - 17:03, UnknownUser
ProgressReportHu in ABI
Page ProgressReportHu The purpose of this page is to make a schedule for my research progress and work plan for the next six months or more. Research progress a…
09 Aug 2023 - 17:03, UnknownUser
ProgressReportHu-05-2011 in ABI
Page ProgressReportHu 05 2011 The purpose of this page is to make a schedule for my research progress and work plan for the next six months or more. Work perfor…
09 Aug 2023 - 17:03, UnknownUser
ProgressReportHu-10-2012 in ABI
Page ProgressReportHu 10 2012 The purpose of this page is to make a schedule for my research progress and work plan for the next six months or more. Work perfor…
09 Aug 2023 - 17:03, UnknownUser
ProgressReportSiragusaFall2010 in ABI
Page ProgressReportSiragusaFall2010 This is the progress report of Enrico Siragusa for the Fall 2010. Accomplishments up to the Fall 2010 * Familiarized with …
09 Aug 2023 - 17:03, UnknownUser
ProgressReportSiragusaSpring2011 in ABI
Page ProgressReportSiragusaSpring2011 This is the progress report of Enrico Siragusa for the Spring 2011. Accomplishments up to the Fall 2010 Literature Seeds …
09 Aug 2023 - 17:03, UnknownUser
Projektseminar_Advanced_Sequence_Analysis_2013 in ABI
Praxismodule Applied Sequence Analysis Welcome to the Wiki of the Praxisseminar Applied Sequence Analysis News Times and rooms Rooms and timings Event …
09 Aug 2023 - 17:03, UnknownUser
ProtLec0MaterialsWS14 in ABI
Learning units No learning units for the introductory lecture. Please see the materials for Lecture 1 for the first units. Lectures 00_CPM_WS14_Introduction 00_C…
09 Aug 2023 - 17:03, UnknownUser
ProtLec10MaterialsWS14 in ABI
Learning units Learning unit 10A to Protein post translational modifications Learning unit 10B to Exptl. techniques for phosphoproteomics Learning unit 10C to Alg…
09 Aug 2023 - 17:03, UnknownUser
ProtLec11MaterialsWS14 in ABI
Learning units Learning unit 11A to Metabolomics and Metabolites Learning unit 11B to Metabolite Databases Learning unit 11C to Metabolite ID via Spectral Matchin…
09 Aug 2023 - 17:03, UnknownUser
ProtLec12MaterialsWS14 in ABI
Learning units Lecture slides Lecture slides (PPT) Lecture slides (PDF) Exercises Videos
09 Aug 2023 - 17:03, UnknownUser
ProtLec1MaterialsWS14 in ABI
Learning units Learning unit 1A to Introduction to Proteomics and Metabolomics Learning unit 1B to Overview of separation techniques Learning unit 1C to Introduct…
09 Aug 2023 - 17:03, UnknownUser
ProtLec2MaterialsWS14 in ABI
Learning units Learning unit 2A to Chromatography (updated) Learning unit 2B to Mass spectrometry Lecture slides Lecture slides Exercises Exercises about separ…
09 Aug 2023 - 17:03, UnknownUser
ProtLec3MaterialsWS14 in ABI
Learning units Learning unit 3A to Basic Statistics Learning unit 3B to Mixture Models and EM Algorithm Lecture slides Lecture slides (PPT) Lecture slides (PDF…
09 Aug 2023 - 17:03, UnknownUser
ProtLec4MaterialsWS14 in ABI
Learning units Learning unit 4A to Basic Analytical Chemistry Learning unit 4B to Quantification strategies (SWATH, TMT, MRM/AQUA, … ) Learning unit 4C to Isoba…
09 Aug 2023 - 17:03, UnknownUser
ProtLec5MaterialsWS14 in ABI
Learning units Learning unit 5A to Label free quantification Learning unit 5B to Map alignment Learning unit 5C to SILAC quantification Lecture slides Lecture s…
09 Aug 2023 - 17:03, UnknownUser
ProtLec6MaterialsWS14 in ABI
Learning units Learning unit 6A to SRM/MRM Learning unit 6B to MRM and Skyline (Tool) Learning unit 6C to SWATH and OpenSWATH (Tool) Lecture slides Lecture slid…
09 Aug 2023 - 17:03, UnknownUser
ProtLec7MaterialsWS14 in ABI
Learning units Learning unit 7A to Peptide database search Learning unit 7B to Tools for database earch (Tool) Learning unit 7C to FDR estimation Learning unit 7D…
09 Aug 2023 - 17:03, UnknownUser
ProtLec9MaterialsWS14 in ABI
Learning units Learning unit 9A to Protein inference problem Learning unit 9B to ProteinProphet Learning unit 9C to Protein FDR estimates Lecture slides Lecture…
09 Aug 2023 - 17:03, UnknownUser
ProteinID in ABI
Page ProteinID Progress reports Progress report fall 2010 Section 2 ((content)) Comments MajorRevisionAntilope MyTodos
09 Aug 2023 - 17:03, UnknownUser
ProteinStructure in ABI
Proteinstrukturen Vorlesungen Date Lecture* *Materials 30.1.2012 Elemente der Strukturbiologie (Krause) Structural Biology 1.2.2012 Review …
09 Aug 2023 - 17:03, UnknownUser
ProteomeAnalysis in ABI
Proteomics Vorlesungen Date Lecture* *Materials 18.1.2012 Einführung HPLC/MS Intro 23.1.2012 Quantitative Proteomics CPM_WS11_05_Quant_I.pdf…
09 Aug 2023 - 17:03, UnknownUser
ProteomicS_SS14 in ABI
Proteomics, SoSe 2014 (19577) Welcome to the Wiki of the MSc seminar Proteomics. In this seminar we will discuss original articles that deal with the analysis of …
09 Aug 2023 - 17:03, UnknownUser
ProteomicsVL_WS14 in ABI
Forschungsmodul: Proteomics VL UE (WiSe 2014) Welcome to the Wiki of the MSc lecture Proteomics (VL: 19400901, UE: 19400902) In this lecture we will cover the ba…
09 Aug 2023 - 17:03, UnknownUser
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